In the summer of 2006, Mr. Steve Lee and Father Edward Hathaway, then pastor of St. John the Baptist Roman Catholic Church in Front Royal, began discussions about founding an independent school that would serve families interested in an education rooted in the liberal arts and the Catholic faith. Having been recently assigned to St. John the Baptist, Father Hathaway was struck by both the great number of Catholic young people in the parish and neighboring parishes and the fact that the closest Catholic high school to Front Royal was nearly an hour away. With children of his own approaching high school age, Mr. Lee was eager to be part of starting a school that would meet the apparent need. In the months following a feasibility study conducted by Mr. Bart Beasley in the winter of 2006-2007, Fr. Hathaway and Mr. Lee formed a board, hired Mr. Jonathan Brand as the founding headmaster, and prepared to open Chelsea Academy in 2008.

As part of the preparations, the board, Mr. Brand, and several parents organized a dinner-auction gala that attracted one-hundred and thirty people and served to generate support and raise money for the school in the spring of 2008.

Chelsea Academy opened with thirty seven students in grades six through nine with plans to add an additional grade over the next three years. Five-full time, three-part time, and two staff members made up the initial faculty and staff. With the addition of four new students in the spring semester, Chelsea finished its first year with forty-one students, all of whom were challenged to grow and develop themselves in and outside of the classroom in a variety of ways. The academic program proved to be challenging and inspiring. Interscholastic sports teams, including soccer, volleyball, basketball, and baseball, were established. A school choir was formed. Houses and clubs met weekly. Mass was held every Friday. Highlights of the year included an all-school hike, a poetry recitation and music recital, a spiritual retreat, a choir concert, a canoe trip, a spring play, and the second-annual spring gala.

Since its first year in 2008, Chelsea has added grades four and five in addition to ten through twelve and has attracted families from Front Royal, Rappahannock County, Winchester, Warrenton, Haymarket, Gainesville, Fort Valley, and Strasburg among other areas. Its programs have expanded to include participation in regional and national poetry, math, and science competitions, and Chelsea sports teams now participate in the Delaney Athletic Conference. Chelsea was accredited by the Virginia Independent Schools Association in 2011. In 2012, eight students received diplomas as members of the school’s first graduating class.

On December 8, 2020, the Feast of the Immaculate Conception, Bishop Michael Burbidge recognized Chelsea Academy as an independent Catholic school in the Diocese of Arlington.